They can do random checks. Its a condition on your firearms certificate if you caught with to many you could lose your license.
When you buy ammo the amount is recorded on your certificate.

How often do they do these random checks? Personally I don't keep all of my eggs in one basket, if you catch my drift. What they would see is only what I want them to see. What would prevent you from going to the range and claiming you fired off all 1000 that are on the books and buying some more? Do they monitor you at the range? What about reloading components? (or can you reload your own ammo there?)

'Japan prohibits handgun possession by citizens. Shotguns and rifles for hunting or sports may be possessed upon completion of a licensing procedure that requires a police background check, successful completion of a safety course, passing of shooting, written, and psychological tests, and police verification of secure storage, prior to approval being granted by the police to purchase a firearm. Fully automatic weapons are restricted to military and police. Gun owners must take a class once a year and pass a written test. Police check on the owner once every three months on an unannounced visit. They inspect the gun locker, proper ammunition storage, and the firearm.' From Wiki

What they DON'T mention here is that they, 'hunters' at least, are only allowed to have I think it is 20 rounds of ammunition and must account for/turn in every shell casing when they want to replenish it.